During early development of the central nervous system (CNS), there is an exuberant outgrowth of projections which later need to be refined to achieve precise connectivity. One widely used strategy for this refinement is axon pruning. Axon pruning has also been suggested to be involved in creating more diverse connection patterns between different species. An understanding of the mechanism of pruning, however, has been elusive in the CNS. Recent studies have focused on a stereotyped pruning event that occurs within the mossy fibers of the developing vertebrate hippocampus. In the following discussion, we will review the cellular and molecular factors that are known to regulate pruning in the hippocampus and highlight some advantages this system presents for future studies on pruning in the developing CNS.